Development and Clinical Validation of Iso-IMRS: A Novel Diagnostic Assay for P. falciparum Malaria

Improving gonorrhoea molecular diagnostics: Genome mining-based identification of identical multi-repeat sequences (IMRS) in Neisseria gonorrhoeae

Background

Curable sexually transmitted infections (STIs), such as Neisseria gonorrhoeae (N. gonorrhoeae), are a major cause of poor pregnancy outcomes. The infection is often asymptomatic in pregnant women, and a syndrome-based approach of testing leads to a missed diagnosis. Culture followed by microscopy is inadequate and time-consuming. The gold standard nucleic acid amplification tests require advanced infrastructure settings, whereas point-of-care tests are limited to immunoassays with sensitivities and specificities insufficient to accurately diagnose asymptomatic cases. This necessitates the development and validation of assays that are fit for purpose.

Methods

We identified new diagnostic target biomarker regions for N. gonorrhoeae using an algorithm for genome mining of identical multi-repeat sequences (IMRS). These were then developed as DNA amplification primers to design better diagnostic assays. To test the primer pair, genomic DNA was 10-fold serially diluted (100 pg/μL to 1 × 10-3 pg/μL) and used as DNA template for PCR reactions. The gold standard PCR using 16S rRNA primers was also run as a comparative test, and both assay products were resolved on 1% agarose gel.

Results

Our newly developed N. gonorrhoeae IMRS-PCR assay had an analytical sensitivity of 6 fg/μL representing better sensitivity than the 16S rRNA PCR assay with an analytical sensitivity of 4.3096 pg/μL. The assay was also successfully validated using clinical urethral swab samples. We further advanced this technique by developing an isothermal IMRS, which was both reliable and sensitive for detecting cultured N. gonorrhoeae isolates at a concentration of 38 ng/μL. Combining isothermal IMRS with a low-cost lateral flow assay, we were able to detect N. gonorrhoeae amplicons at a starting concentration of 100 pg/μL.

Conclusion

Therefore, there is a potential to implement this concept within miniaturized, isothermal, microfluidic platforms, and laboratory-on-a-chip diagnostic devices for highly reliable point-of-care testing.

Development and application of a universal extraction-free reagent based on an algal glycolipid

In this study, we independently developed a universal nasopharyngeal swab extraction-free reagent based on a trehalose lipid for the rapid detection of pathogen nucleic acids in respiratory infectious diseases. By comparing the isothermal amplification results of a 2019-nCoV pseudovirus solution treated with different components of the extraction-free reagent, we determined the optimal composition of the extraction-free reagent to be a mixed solution of 10 mmol L-1 tris-HCl containing 0.05 mmol L-1 EDTA (TE solution), 5% glycine betaine, 0.5% Triton X-100, and 1.5% trehalose lipid. The results showed that the extraction-free reagent could cleave DNA viruses, RNA viruses, and bacteria to release nucleic acids and did not affect the subsequent nucleic acid amplification. Its efficiency was consistent with that of magnetic bead extraction. Real-time fluorescence quantitative PCR was used to analyze the stability and repeatability of the detection results of the samples treated with the extraction-free reagent and the sensitivity of the extraction-free reagent. The results showed that the extraction-free kit could stably store the pathogen nucleic acid for at least 24 hours, the detection repeatability was satisfactory, and there was no incompatibility with the detection limits of various manufacturers' nucleic acid detection reagents. In conclusion, the established nucleic acid extraction-free method can effectively lyse respiratory infectious disease pathogens to release nucleic acids (DNA and RNA) at room temperature and can directly amplify nucleic acids without extraction steps. This method takes a short time and has high efficiency. The released nucleic acid met the requirements of molecular biological detection methods such as real-time fluorescence quantitative PCR (qPCR), reverse transcription-polymerase chain reaction (RT-PCR), and isothermal nucleic acid amplification (INAA).

Strategies for Engineering Affordable Technologies for Point-of-Care Diagnostics of Infectious Diseases

Disease prevalence is highest in low-resource settings (LRS) due to the lack of funds, infrastructure, and personnel required to carry out laboratory-based molecular tests. In high-resource settings, gold-standard molecular tests for diseases consist of nucleic acid amplification tests (NAATs) due to their excellent sensitivity and specificity. These tests require the extraction, amplification, and detection of nucleic acids from clinical samples. In high-resource settings, all three of these steps require highly specialized, costly, and onerous equipment that cannot be used in LRS. Nucleic acid extraction involves multiple centrifugation steps. Amplification consists of the polymerase chain reaction (PCR), which requires thermal cyclers. The detection of amplified DNA is typically done with specialized thermal cyclers that are capable of fluorescence detection. Traditional methods used to extract, amplify, and detect nucleic acids cannot be used outside of a laboratory in LRS. Thus, there is a need for affordable point-of-care devices to ease the high burden of disease in LRS.The past decade of work on paper-based fluidic devices has resulted in the invention of many paper-based biosensors for disease detection as well as isothermal amplification techniques that replace PCR. However, a challenge still remains in detecting pathogenic biomarkers from complex human samples without specialized laboratory equipment. Our research has focused on the development of affordable technologies to extract and detect nucleic acids in clinical samples with minimal equipment. Here we describe methods for the paper-based extraction, amplification, and detection of nucleic acids. This Account provides an overview of our latest technologies developed to detect an array of diseases in low-resource settings. We focus on detecting nucleic acids of H1N1, human papillomavirus (HPV), Neisseria gonorrheae (NG), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV), and malaria from a variety of clinical sample types. H1N1 RNA was extracted from nasopharyngeal swabs; HPV, NG, and CT DNA were extracted from either cervical, urethral, or vaginal swabs; TV DNA was extracted from urine; and malaria DNA was extracted from whole blood. Different sample types necessitate different nucleic extraction protocols; we provide guidelines for assay design based on the clinical sample type used. We compare the pros and cons of different isothermal amplification techniques, namely, helicase-dependent amplification (HDA), loop-mediated isothermal amplification (LAMP), and a novel isothermal amplification technique that we developed: isothermal-identical multirepeat sequences (iso-IMRS). Finally, we compare various detection mechanisms, including lateral-flow and electrochemical readouts. Electrochemical readouts frequently employ gold electrodes due to strong gold-thiol coupling. However, the high cost of gold precludes their use in LRS. We discuss our development of novel gold leaf electrodes that can be made without specialized equipment for a fraction of the cost of commercially available gold electrodes.